W08-PSYC-250-01: methodology of research 2008

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IMPORTANT NOTES!! Please contact the speaker or course instructors if you would like to use any of the slides. Some slides have been borrowed from SPM, FSL or related websites, and should be referenced appropriately when used.

Winter 2008 -Neuroimaging-

When: Fridays 12:15pm - 2:00pm (January 11th to March 14th)

Where: Room 2213, Psychiatry Bldg

Instructor: Fumiko Hoeft MD PhD (fumiko'at'stanford'dot'edu), Sen Res Sci, CIBSR

Co-Instructor: Brian W. Haas PhD (bhaas'at'stanford'dot'edu), Postdoc, CIBSR

This course is intended for novices to neuroimaging research or those who want to be intelligent consumers. The Winter quarter will begin by introducing various functional and structural neuroimaging research methods (e.g. functional magnetic resonance imaging (fMRI), structural MRI (sMRI), diffusion tensor imaging (DTI), transcranial magnetic stimulation (TMS), near-infrared spectroscopy (NIRS), electroencephalogram (EEG)). Basic principles, statistical analysis methods, advantages and limitations, and applications will be discussed. Later in the quarter, there will be tutorials where participants analyze sample data. By the end of the class, participants are expected to become more familiar with the scientific questions addressed using neuroimaging and be able to read neuroimaging papers more critically.

Weekly Schedule (subject to change)

Week 1 (January 11) Introduction:
Introduction of course and clinical utility of neuroimaging methods (Fumiko Hoeft)
1. class slides
2. reading: Applications of fMRI in translational medicine and clinical practice (Matthews et al. Nat Rev Neurosci '06)
3. reading: Chapter 1 from Statistical Parametric Mapping, Academic Press, 2007
4. reading: introductory slides to various neuroimaging techniques (courtesy of Allan Reiss)
Week 2 (January 18) Basic principles of MRI:
MR physics, and physiological basis (Gary Glover)
video available, please contact Brian
1. class slides
2. supplemental slides

Week 3 (January 25) Functional MRI:
Utilization of techniques, spatial and temporal resolution, task design, and how data is processed (Brian Haas, Fumiko Hoeft)
1. reading: Chapter 2 from Statistical Parametric Mapping, Academic Press, 2007
2. reading: Functional and morphometric brain dissociation between dyslexia and reading ability (Hoeft et al. PNAS '07)
3. class slides (task design etc)
4. class slides

Week 4 (February 1) Statistics:
Introduction to software, general linear model, and single subject and group analysis (Fumiko Hoeft)
1. reading: Chapter 3 from Statistical Parametric Mapping, Academic Press, 2007
2. class slides

Week 5 (February 8) Functional connectivity:
Theoretical rationale, functional and effective connectivity, and utilizing EEG in combination with fMRI (Vinod Menon)
1. class slides

Week 6 (February 15) LAB - Application using sample data:
Each student will process and analyze a set of fMRI data (Brian Haas)

Week 7 (February 22) Structural MRI:
Volumetric analysis, voxel-wise analysis of finer resolution, and more sophisticated analyses such as cortical mapping and gyrification (Allan Reiss)
video available, please contact Brian
1. class slides

Week 8 (February 29) Diffusion Tensor Imaging:
Theoretical rationale, acquisition and analysis techniques (Robert Dogherty)
video available, please contact Brian
1. reading: Le Bihan et al. JMRI 2006
2. reading: Beaulieu. NMR Biomed 2002
3. reading: Jellison et al. AJNR 2004
4. class slides

Week 9 (March 7) Other techniques (TMS, NIRS, PET, SPECT, MRS)
Overview of other neuroimaging methods (Fumiko Hoeft, Amy Garrett, Manpreet Singh)
1. class slides (MRS)
2. class slides (PET, SPECT)
3. class slides (TMS, NIRS)

Week 10 (March 14) Summary & Discussion of Some Papers of Interest (+ NIRS)
(Fumiko Hoeft, Brian Haas)
1. class slides (summary)
i) Brain Dynamics Underlying the Nonlinear Threshold for Access to Consciousness (PloS Biol '07) - Fumiko & Shelley Hill
ii) Disruption of Large-Scale Brain Systems in Advanced Aging (Neuron '07) - Brian & Joy Taylor
iii) Automated cortical thickness measurements from MRI can accurately separate Alzheimerfs patients from normal elderly controls (Neurobiol Aging '08) & related paper by Wes Ashford (J Nucl Med '00) - Fumiko & Wes Ashford
iv) Regional Dynamics of the fMRI-BOLD Signal Response to Hypoxia-Hypercapnia in the Rat Brain (J MRI '03) - Brian & Hitha Amin

Guest Speakers

Robert Dougherty PhD, Sen Res Sci, Psychology
Amy Garrett PhD, Res Assoc, CIBSR
Gary Glover PhD, Prof, Director, Radiology, Lucas Imaging Center
Vinod Menon PhD, Assoc Prof, Director, Cog & Syst Neurosci Lab
Allan Reiss MD, Prof, Director, CIBSR
Manpreet Singh MS MD, Clinical Instructor & Postdoc, CIBSR